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CHARMM preflx directives
#182 10/21/03 02:32 PM
Joined: Oct 2003
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tjaart Offline OP
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I don't seem to understand the manual. With which preflx directives should I compile CHARMM for a Linux cluster running MPI? We have verified that MPI is working yet a simple command like building the psf file takes more than an hour and then it fails with:
fmt: read unexpected character
apparent state: unit 27 named pdb.psf
last format: (818)
lately reading sequential formatted external IO

Can anyone help?
Thanks!!


Tjaart de Beer
Re: CHARMM preflx directives
tjaart #183 10/21/03 03:34 PM
Joined: Sep 2003
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If you have been playing with the installation, you have to be aware that if there is already a build/gnu/pref.dat it will be used unmodified, even if you give new arguments to install.com. Changes in pref.dat (either manually introduced, or by install.com if you first delete the old pref.dat) are NOT picked up by the Makefile, so unless you know exactly what you are doing you should remove all files in lib/gnu when you make changes to pref.dat before running install.com again.
Then this should work:
install.com gnu medium M MPICH

If all you do is to generate a psf it should not take one hour. Your brief message seems to indicate that you are actually reading the psf - are you having some sort of I/O problem in your system? Does this happen when you run on one CPU also?


Lennart Nilsson
Karolinska Institutet
Stockholm, Sweden

Moderated by  lennart, rmv 

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